Submitted to Ecology Letters, Evolution or Evolution Letters – well let’s see what we find!
Affiliations: 1Department of Bioscience, Durham University, Stockton Rd., Durham DH1 3LE, UK. 2University of Sao Paulo, xxxxx. 3Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
Correspondence: *guillaume.chomicki@durham.ac.uk
Analyses accounting for climate
The results below follow the same rationale as the ones from the main document. However, in the cases below all analyses use the plant traits already accounted for climatic effects by using the residuals from the regressions between each trait and the first three Principal Components of the climatic variables obtained from BioClim (REF).
Methods
here::i_am("manuscript/chomicki_et_al_climpc.Rmd")
source(here::here("R/tree_plots.R"))
library("knitr")
library("RColorBrewer")
library("kableExtra")
# load("../output/first_analysis.RData")
knitr::opts_chunk$set(fig.pos = "h", out.extra = "")
# source("../R/ouwie_summary_mcc.R")
pars.table.pc1 <- read.csv(here::here("output/fullpar_table_climpc1.csv"))
pars.table.pc1$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc1$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc2 <- read.csv(here::here("output/fullpar_table_climpc2.csv"))
pars.table.pc2$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc2$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc3 <- read.csv(here::here("output/fullpar_table_climpc3.csv"))
pars.table.pc3$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc3$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
colors <- setNames(brewer.pal(4, "Set1"), 1:4)
sig.formatter <- function(x){cell_spec(x, format = "latex", bold = ifelse(x > 75, TRUE, FALSE), background = if(x >= 90){"red"} else if(x < 90 & x >= 50){"yellow"})}MCC tree
- 1000 reconstructions of each discrete trait (namely Mutualistic Strategy, Presence of Warts, Presence of Reward, Plant Architecture, Domatium growth type, Mating System, Leaf Structure and Presence of appendages)
- Sampled 100 reconstructions and performed continuous trait evolution analysis (Stem Area, Leaf Area, Corolla Length and Petiole Length) using residuals of correlations between continuous traits and the first 3 climatic PCs.
- Fitted 7 models:
- Single-rate Brownian Motion (BM1 - 1 parameter)
- Multiple-rate Brownian Motion (BMS - 3 parameters)
- Simple OU (OU1 - 3 parameters)
- OU with different optima but same alpha and sigma (OUM - 5 parameters)
- OU with different optima and alpha but same sigma (OUMA - 7 parameters)
- OU with different optima and sigma but same alpha (OUMV - 7 parameters)
- OU with different optima, alpha, and sigma (OUMVA - 9 parameters)
Results
Ancestral State Reconstruction of Mutualistic Strategy
The following figure represents the summary of 1000 stochastic maps for each discrete trait, that were summarized for each node.
Evolution of continuous traits based on states of discrete traits
Lastly, we fitted all 7 models of leaf area evolution to 10 sampled evolutionary histories of mutualistic strategy. Due to the elevated number of variables and models, we opted to use a model averaging approach by calculating the weighted average of parameter values. The final value of each parameter was calculated by multiplying the estimated value for a given parameter in a given model by the Akaike weight of the given model. Thus, we need not resort to any arbitrary criterium (such as \(\delta\)AIC > 2) and can evaluate the dynamics solely based on the parameter values.
All plots below were filtered to exclude parameter values that were larger than -10 (\(e^-10\)) and smaller than 10 (\(e^10\)), on the justification of representing bad fitting or unreasonable biological meaning.
Appendages
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
PC3 - Parameter differences
Architecture
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
PC3 - Parameter differences
Domatium Growth
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
PC3 - Parameter differences
Leaf Structure
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
PC3 - Parameter differences
Mating System
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
PC3 - Parameter differences
Reward
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
PC1 - Parameter differences
PC2 - Parameter
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
PC3 - Parameter differences
Strategy
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
PC3 - Parameter differences
Warts
PC1 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.
PC1 - Parameter differences
PC2 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.
PC2 - Parameter differences
PC3 - Parameters
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.